I've used Arduino a bit on both Windows/Linux, but haven't seen this issue before.
On a Windows 7 64bit Pro laptop, the Arduino IDE appears to constantly open/close the COM ports which naturally causes the Arduino to reset.
This happens many times a second, you can see the P13 LED flash rapidly as soon as you open the Arduino IDE (version 1.6.8).
Closing the IDE stops the issue.
Another artifact of the issue is that it's difficult to program the Arduino reliably as often you get this error:
avrdude: ser_open(): can't open device "\.\COM16": Access is denied.
If you retry enough times, it eventually works.
Any ideas what's going on?
I am using a SparkFun RedBoard with a built in FTDI chip.